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Volumn 11, Issue , 2010, Pages

Fine-tuning structural RNA alignments in the twilight zone

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPLE SEQUENCE ALIGNMENTS; SECONDARY STRUCTURES; SEQUENCE ALIGNMENTS; SEQUENCE IDENTITY; SEQUENCE SIMILARITY; STRUCTURAL ALIGNMENTS; STRUCTURE ALIGNMENT; TWILIGHT ZONE;

EID: 77953653729     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-222     Document Type: Article
Times cited : (13)

References (33)
  • 1
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • 526219, 15458580
    • Gardner P, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004, 5(140). 526219, 15458580.
    • (2004) BMC Bioinformatics , vol.5 , Issue.140
    • Gardner, P.1    Giegerich, R.2
  • 2
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM Journal of Applied Mathematics 1985, 45:810-825.
    • (1985) SIAM Journal of Applied Mathematics , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 3
    • 16344363338 scopus 로고    scopus 로고
    • Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
    • 10.1093/bioinformatics/bti279, 15657094
    • Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 2005, 21(9):1815-1824. 10.1093/bioinformatics/bti279, 15657094.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1815-1824
    • Havgaard, J.H.1    Lyngso, R.B.2    Stormo, G.D.3    Gorodkin, J.4
  • 4
    • 34249699636 scopus 로고    scopus 로고
    • Multiple structural alignment and clustering of RNA sequences
    • 10.1093/bioinformatics/btm049, 17324941
    • Torarinsson E, Havgaard JH, Gorodkin J. Multiple structural alignment and clustering of RNA sequences. Bioinformatics 2007, 23:926-932. 10.1093/bioinformatics/btm049, 17324941.
    • (2007) Bioinformatics , vol.23 , pp. 926-932
    • Torarinsson, E.1    Havgaard, J.H.2    Gorodkin, J.3
  • 5
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: an algorithm for finding the secondary structure common to two RNA sequences
    • 10.1006/jmbi.2001.5351, 11902836
    • Mathews DH, Turner DH. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology 2002, 317(2):191-203. 10.1006/jmbi.2001.5351, 11902836.
    • (2002) Journal of Molecular Biology , vol.317 , Issue.2 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 6
    • 34248632816 scopus 로고    scopus 로고
    • Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign
    • 1868766, 17445273
    • Harmanci AO, Sharma G, Mathews DH. Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign. BMC Bioinformatics 2007, 8(130). 1868766, 17445273.
    • (2007) BMC Bioinformatics , vol.8 , Issue.130
    • Harmanci, A.O.1    Sharma, G.2    Mathews, D.H.3
  • 7
    • 5044242515 scopus 로고    scopus 로고
    • Alignment of RNA base pairing probability matrices
    • 10.1093/bioinformatics/bth229, 15073017
    • Hofacker IL, Bernhart SH, Stadler PF. Alignment of RNA base pairing probability matrices. Bioinformatics 2004, 20(14):2222-2227. 10.1093/bioinformatics/bth229, 15073017.
    • (2004) Bioinformatics , vol.20 , Issue.14 , pp. 2222-2227
    • Hofacker, I.L.1    Bernhart, S.H.2    Stadler, P.F.3
  • 8
    • 24144497144 scopus 로고    scopus 로고
    • Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
    • 10.1093/bioinformatics/bti577, 16020472
    • Reeder J, Giegerich R. Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics 2005, 21(17):3516-3523. 10.1093/bioinformatics/bti577, 16020472.
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3516-3523
    • Reeder, J.1    Giegerich, R.2
  • 9
    • 4544339512 scopus 로고    scopus 로고
    • Abstract Shapes of RNA
    • 10.1093/nar/gkh779, 519098, 15371549
    • Giegerich R, Voss B, Rehmsmeier M. Abstract Shapes of RNA. Nucleic Acids Res 2004, 32(16):4843-4851. 10.1093/nar/gkh779, 519098, 15371549.
    • (2004) Nucleic Acids Res , vol.32 , Issue.16 , pp. 4843-4851
    • Giegerich, R.1    Voss, B.2    Rehmsmeier, M.3
  • 12
    • 24044519380 scopus 로고    scopus 로고
    • MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
    • 10.1093/bioinformatics/bti550, 15972285
    • Siebert S, Backofen R. MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 2005, 21(16):3352-3359. 10.1093/bioinformatics/bti550, 15972285.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3352-3359
    • Siebert, S.1    Backofen, R.2
  • 15
    • 0043123123 scopus 로고    scopus 로고
    • Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments
    • 10.1093/nar/gkg522, 168929, 12824354
    • Poirot O, O'Toole E, Notredame C. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res 2003, 31(13):3503-3506. 10.1093/nar/gkg522, 168929, 12824354.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3503-3506
    • Poirot, O.1    O'Toole, E.2    Notredame, C.3
  • 16
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • 10.1093/bib/bbn013, 18372315
    • Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9(4):286-298. 10.1093/bib/bbn013, 18372315.
    • (2008) Brief Bioinform , vol.9 , Issue.4 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 17
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • 10.1093/nar/gkg614, 169020, 12824339
    • Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 2003, 31(13):3423-3428. 10.1093/nar/gkg614, 169020, 12824339.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 18
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • 10.1016/S0022-2836(02)00308-X, 12079347
    • Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences. J Mol Biol 2002, 319(5):1059-1066. 10.1016/S0022-2836(02)00308-X, 12079347., http://dx.doi.org/10.1016/S0022-2836(02)00308-X
    • (2002) J Mol Biol , vol.319 , Issue.5 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 19
    • 36549056971 scopus 로고    scopus 로고
    • RNA consensus structure prediction with RNAalifold
    • Hofacker IL. RNA consensus structure prediction with RNAalifold. Methods Mol Biol 2007, 395:527-544.
    • (2007) Methods Mol Biol , vol.395 , pp. 527-544
    • Hofacker, I.L.1
  • 20
    • 3242880117 scopus 로고    scopus 로고
    • ILM: a web server for predicting RNA secondary structures with pseudoknots
    • Web Server
    • Ruan J, Stormo GD, Zhang W. ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res 2004, (32 Web Server):146-149.
    • (2004) Nucleic Acids Res , Issue.32 , pp. 146-149
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 21
    • 44649166879 scopus 로고    scopus 로고
    • ConStruct: improved construction of RNA consensus structures
    • 2408607, 18442401
    • Wilm A, Linnenbrink K, Steger G. ConStruct: improved construction of RNA consensus structures. BMC Bioinformatics 2008, 9(219). 2408607, 18442401.
    • (2008) BMC Bioinformatics , vol.9 , Issue.219
    • Wilm, A.1    Linnenbrink, K.2    Steger, G.3
  • 22
    • 34547844102 scopus 로고    scopus 로고
    • Murlet: a practical multiple alignment tool for structural RNA sequences
    • 10.1093/bioinformatics/btm146, 17459961
    • Kiryu H, Tabei Y, Kin T, Asai K. Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 2007, 23(13):1588-1598. 10.1093/bioinformatics/btm146, 17459961.
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 1588-1598
    • Kiryu, H.1    Tabei, Y.2    Kin, T.3    Asai, K.4
  • 23
    • 41749122381 scopus 로고    scopus 로고
    • A fast structural alignment method for long RNA sequences
    • 2375124, 18215258
    • Tabei Y, Kiryu H, Kin T, Asai K. A fast structural alignment method for long RNA sequences. BMC Bioinformatics 2008, 9(33). 2375124, 18215258.
    • (2008) BMC Bioinformatics , vol.9 , Issue.33
    • Tabei, Y.1    Kiryu, H.2    Kin, T.3    Asai, K.4
  • 24
    • 48449091195 scopus 로고    scopus 로고
    • WAR: Webserver for aligning structural RNAs
    • Web server, 10.1093/nar/gkn275, 2447782, 18492721
    • Torarinsson E, Lindgren S. WAR: Webserver for aligning structural RNAs. NAR 2008, (36 Web server):W79-W84. 10.1093/nar/gkn275, 2447782, 18492721.
    • (2008) NAR , Issue.36
    • Torarinsson, E.1    Lindgren, S.2
  • 25
    • 17844386108 scopus 로고    scopus 로고
    • A benchmark of multiple sequence alignment programs upon structural RNAs
    • 10.1093/nar/gki541, 1087786, 15860779
    • Gardner PP, Wilm A, Washietl S. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research 2005, 33(8):2433-2439. 10.1093/nar/gki541, 1087786, 15860779.
    • (2005) Nucleic Acids Research , vol.33 , Issue.8 , pp. 2433-2439
    • Gardner, P.P.1    Wilm, A.2    Washietl, S.3
  • 26
    • 4143149651 scopus 로고    scopus 로고
    • Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
    • 10.1016/j.jmb.2004.07.018, 15313604
    • Washietl S, Hofacker I. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 2004, 342. 10.1016/j.jmb.2004.07.018, 15313604.
    • (2004) J Mol Biol , vol.342
    • Washietl, S.1    Hofacker, I.2
  • 27
    • 14044272835 scopus 로고    scopus 로고
    • Fast and reliable prediction of noncoding RNAs
    • 10.1073/pnas.0409169102, 548974, 15665081
    • Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci 2005, 102(7):2454-2459. 10.1073/pnas.0409169102, 548974, 15665081.
    • (2005) Proc Natl Acad Sci , vol.102 , Issue.7 , pp. 2454-2459
    • Washietl, S.1    Hofacker, I.L.2    Stadler, P.F.3
  • 28
    • 42949090850 scopus 로고    scopus 로고
    • Strategies for measuring evolutionary conservation of RNA secondary structures
    • 10.1186/1471-2105-9-122, 2335298, 18302738
    • Gruber AR, Bernhart SH, Hofacker IL, Washietl S. Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics 2008, 9:122. 10.1186/1471-2105-9-122, 2335298, 18302738.
    • (2008) BMC Bioinformatics , vol.9 , pp. 122
    • Gruber, A.R.1    Bernhart, S.H.2    Hofacker, I.L.3    Washietl, S.4
  • 29
    • 58249121729 scopus 로고    scopus 로고
    • RNAalifold: Improved Consensus Structure Prediction for RNA Alignments
    • 10.1186/1471-2105-9-474, 2621365, 19014431
    • Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: Improved Consensus Structure Prediction for RNA Alignments. BMC Bioinformatics 2008, 9:474. 10.1186/1471-2105-9-474, 2621365, 19014431.
    • (2008) BMC Bioinformatics , vol.9 , pp. 474
    • Bernhart, S.H.1    Hofacker, I.L.2    Will, S.3    Gruber, A.R.4    Stadler, P.F.5
  • 31
    • 84888275115 scopus 로고    scopus 로고
    • BRAliBase
    • BRAliBase. , http://projects.binf.ku.dk/pgardner/bralibase/
  • 32
    • 13444252847 scopus 로고    scopus 로고
    • Rfam: annotating non-coding RNAs in complete genomes
    • Database, 540035, 15608160
    • Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005, (33 Database):D121-D124. 540035, 15608160., http://view.ncbi.nlm.nih.gov/pubmed/15608160
    • (2005) Nucleic Acids Res , Issue.33
    • Griffiths-Jones, S.1    Moxon, S.2    Marshall, M.3    Khanna, A.4    Eddy, S.R.5    Bateman, A.6
  • 33
    • 0036084598 scopus 로고    scopus 로고
    • 5S Ribosomal RNA Database
    • 10.1093/nar/30.1.176, 99124, 11752286
    • Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5S Ribosomal RNA Database. Nucleic Acids Res 2002, 30:176-178. 10.1093/nar/30.1.176, 99124, 11752286., http://view.ncbi.nlm.nih.gov/pubmed/11752286
    • (2002) Nucleic Acids Res , vol.30 , pp. 176-178
    • Szymanski, M.1    Barciszewska, M.Z.2    Erdmann, V.A.3    Barciszewski, J.4


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